We've had reports of the side chain selection disappearing for users. Here's why, and how to fix it.
This issue seems to be caused by an intermittent error in Apple's 'AuVal' process when scanning plug-ins in Logic, which sometimes mistakes plug-ins that include an external side-chain feature to not be side-chain compatible. This can most often be solved by forcing a AU plug-in reset.
Step-by-Step Solution
Go to the plugin manager in Logic [Settings > Plugin Manager]
Select "Full Audio Unit Reset"
Quit Logic
Open Logic, which will trigger the re-scan again.